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GenBank
There are • GenBank is a sequence database that
contains a collection of annotated nucleic
several acid sequence data.
nucleotide • It includes various types of genetic
databases. material, such as genomic DNA, messenger
Some of the RNA (mRNA), complementary DNA (cDNA),
expressed sequence tags (ESTs), high-
most popular throughput raw sequence data, and
nucleotide sequence polymorphisms.
databases are:
• GenBank and its collaborators receive
sequences produced in laboratories
throughout the world from more than
500,000 formally described species.
GenBank
• GenBank has become an important database
for research in biological fields and has
grown in recent years at an exponential
rate by doubling roughly every 18 months.
• https://www.ncbi.nlm.nih.gov/genbank/
Protein database
• Protein databases are a type of biological database that are collections of information about
proteins.
• The information contained in protein databases includes the amino acid sequence, the
domain structure, the biological function of the protein, its three-dimensional structure, and
its interactions with other proteins.
• Several protein databases are publicly available. Based on the type of information stored,
protein databases can be classified into several categories. Some of the most common
categories of protein databases are as follows:
• Sequence Databases, Structure Databases, Interaction Databases, Functional Annotation
Databases, Disease-Associated Databases, Expression Databases
Protein Sequence Databases
• The protein sequence database contains amino acid sequences of proteins and related
information. The amino acid sequence of a protein is important because it determines the
protein’s three-dimensional structure and function, as well as its identity.
Some of the most popular protein sequence databases are:
SWISS-PROT
• SWISS-PROT is a protein sequence database that provides high levels of
annotations, including information on the protein’s function, domain
structure, post-translational modifications, and variants.
• Swiss-Prot is jointly managed by the SIB (Swiss Institute of Bioinformatics)
and the EBI (European Bioinformatics Institute).
• The database distinguishes itself from other protein sequence databases by
three criteria: (i) annotations, which cover a broad range of information, (ii)
minimal redundancy, which ensures that each sequence is represented only
once, and (iii) integration with other databases, which enables cross-
referencing and retrieval of information from related databases.
• https://www.uniprot.org/
DATA RETRIEVAL
TOOLS:
• In databases, data
retrieval is the
process of identifying
and extracting data
from a database,
based on a query
provided by the user
or application.
Entrez
• Entrez is an integrated search engine which allows
users to search and retrieve different data from the
National Center for Biotechnology Information
(NCBI).
• It can be accessed from the
site www.ncbi.nlm.nih.gov/Entrez/.
• Entrez is NCBI’s major text search and retrieval
system which integrates PubMed database and 39
other scientific literatures, nucleotide and protein
databases, protein domain data, population study
datasets, expression data, pathways and systems of
interacting molecules, complete genome details and
taxonomic information into a tightly inter linked
system.
TAXONOMY BROWSER:
• The Taxonomy Browser is a synthetic database that allows users to
examine the progress of DNA barcoding by browsing through the
different levels of the taxonomic hierarchy available on BOLD.
• Within the Taxonomy Browser, users can select phlya in the Animal,
Plant, Fungus, or Protist kingdoms to navigate from phylum to
species level. Statistics on the progress of DNA barcoding at each
taxon are generated from both public and private data while
protecting private user-owned data.
• Database allows browsing of the taxonomy tree, which contains a
classification of organisms.
• https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi
• https://v3.boldsystems.org/index.php/resources/handbook?chapter=2_datab
ases.html§ion=tax_browser